This is the main function to access slot data for all genes as a sparse matrix.
Usage
GetSparseMatrix(
data,
mode.slot = DefaultSlot(data),
columns = NULL,
genes = Genes(data),
name.by = "Symbol"
)Arguments
- data
A grandR object
- mode.slot
Which kind of data to access (see details)
- columns
which columns (i.e. samples or cells) to return (see details)
- genes
Restrict the output table to the given genes
- name.by
A column name of Coldata(data). This is used as the rownames of the output table
Details
To refer to data slots, the mode.slot syntax can be used: It is either a data slot, or one of (new,old,total) followed by a dot followed by a slot. For new or old, the data slot value is multiplied by ntr or 1-ntr. This can be used e.g. to obtain the new counts.
Columns can be given as a logical, integer or character vector representing a selection of the columns (samples or cells).
The expression is evaluated in an environment havin the Coldata, i.e. you can use names of Coldata as variables to
conveniently build a logical vector (e.g., columns=Condition=="x").